A few reasons.
When the clip on is in front of your day scope, you are allowing it to receive and amplify more existing light. That is why clip ons have catadioptic lenses inside of them (just like a telescope). That in turn, gives you a brighter more crisp image, more FOV, etc. I'm not debating that daytime scopes aren't designed to bring in light, however, they are not whats allowing you to see in the dark. Also, the way clip on's are designed, they work with a large majority of existing daytime scopes. The focusing isn't that technical. There is a large focus knob on the clip on, that you twist until your image crisps up. Same as your daytime optic. It's one more step, but it would be a similar process if the nv were behind the daytime optic.
If you a put night vision device behind a daytime magnified optic, there are a few issues. There isn't really any universal way to mount them, meaning it's not just plug and play-so to speak- like a clip on is. There is also an amount of light degradation, because every time light passes through glass it is degraded slightly. The tube, the key ingredient to the mix, that's doing all the light amplifying is now hindered from amplifying as much existing light as it should be able to because its the very last to get the light. Dont get me wrong, you can still mount a PVS-14 behind a RDO or a ACOG (non tritium) or even a 1-4 or 1-6 variable, but it isn't optimum with those higher magnified optics, and wont get you out to the same distances in a practical manner. Eye relief is another issue. It's hard to get it just right on the rail, and when you do, you find that your daytime optic is pushed far forward on the rail, and now you have a wonky looking setup, and you really aren't going to be able to use in the daytime, because you now have a daytime eye relief issue.